If you look at the evolution of sailboat deck design in the last 40 or 50 years, all sorts of ways have been tried to reduce windage and provide headroom under a deck. The old CCA style of yachts, pretty much all had trunk cabins sticking up through the deck. Some may have had rounded fronts, but they still just pocked through the deck. The side decks were low, crown was increased, bulwarks lowered, extruded toe rails introduced, etc.
Blister style of decks appeared in the early 70's with the introduction of the IOR racers, again to reduce windage, yet still keep the sheer low. Progressively, the new hull forms of these yachts, required the sheer to be raised and a lot more deck crown employed, often designed with a thick deck flange (several inches), further raising the sheer line, to provide headroom below a reasonably sized deck house structure.
Again, there are issues with both approaches (raised deck/trunk cabin). It's a mater of scale. The Cal 20 is just too small to have a reasonable head room below, yet the Flicka, using huge roof crown and deep belly can pull it off. These are aesthetic considerations for the most part, as expecting standing headroom in a 20' Flicka is just a wish for a canoe belly design. This is the rub, between say 20' to 35' on deck with modern, shallow hull forms. You can build the hull down and increase the draft, wetted surface and hull volume, for sufficient headroom without a Winnebago parked on the deck or use some other sort of visual trick, to fool the eye into thinking is not a Winnebago, but just a minivan sitting up there (like Flicka does). Once you get over the small and smaller medium size yachts, you have more then enough hull volume to contain the headroom.
In terms of windage, you want a surfboard with a sail attached, but this doesn't offer much enclosed headroom. Anything bigger does and it's surface area and protrusions that you try to "clean" up. As I mentioned, there's lots of stuff to consider, like stanchion arrangements, which can be ugly on a broken sheer deck line, though they also can be acceptable, if well thought out. Life line arrangements aren't typically given a lot of thought, after they've been sized and spaced appropriately, but the better designers do put some aesthetic consideration into them, some quite clever.
There's no doubt from a structural stand point, flush decks are much stronger, compared to a trunk cabin arrangement on the same hull. It also does make an interior feel much larger, even if the hull shape and typical accommodation setups do limit the practical nature of this increased volume. In the end, the choice can be a practical one, particularly on a small boat or maybe an blue water vessel, looking for every strength advantage it can get.
I have a 50' design with a pilothouse and flush deck. I use the pilothouse as the transition from the standard deck height to the raised portion. It helps mitigate the break in the sheer, with the bulk of the pilothouse obscuring the sheer break. On a 50' - 52' yacht, especially if not performance oriented (the pilothouse suggests it's not), it pretty easy to make a pleasing profile. Trying the same thing on a 35'er will be quite tough, but you can still pull it off, though you'll have to make more design concessions in other areas.
